No, the variation is of proper length. It's true that there can be multiple geodesics between the same pair of events in curved spacetime; but it is also true that a particular event in spacetime plus a particular tangent vector at that event defines a unique geodesic through the entire curved spacetime. The latter method is how the proper length of the arms of the GW detector is defined: the directions of the two interferometer lasers, firing from the same point (the apex of the L-shaped interferometer), define two spatial directions (and therefore two spacelike tangent vectors) at each firing event, and therefore define two unique spacelike geodesics from that event to the simultaneous events at the mirrors--"simultaneous" in the local inertial frame in which the apex of the interferometer is at rest. Integrating the metric along these geodesics gives proper length.
The mirrors are also at rest in the LIF of the apex, in the "resting" state of the detector, but when a GW passes, the mirrors move in this frame; and the change in apex-mirror distance in the LIF corresponds to a change in proper length of each arm, because within the LIF, curves of constant time correspond to spacelike geodesics as defined above, so length along those curves, which is just spatail distance in the LIF, corresponds to proper length.